R packages

PsyGeNET2R

This package allows exploration and analysis of data available in the PsyGeNET database on psychiatric diseases and their genes. It allows the analysis of the user’s data and integrate it with PsyGeNET. The package is available at Bioconductor here.

DisGeNET2R (beta version)

The package contains a series of functions to retrieve and expand gene-disease, and variant-disease data, and to perform mappings of several biomedical vocabularies. The results of the queries can be visualized using a variety of plots, such as heatmaps, barplots and several types of networks. Furthermore, the disgenet2r package permits benefiting from Semantic Web technologies, without the need of special expertise in this area through a set of functions that use DisGeNET-RDF and other resources available in the LOD cloud. These functions include retrieving the druggable targets for a disease of interest, or the pathways associated to a list of diseases. The disgenet2r package also expedites the integration of DisGeNET data with other R/Bioconductor packages. The source code and documentation of disgenet2r package are available at bitbucket

ComoRbidity (beta version)

 

The comoRbidity R package is a new tool for studying disease comorbidity from patient-level data. It allows the identification of disease comorbidity and its subsequent analysis in a clear and easy way. The comoRbidity R package identifies the statistically significant comorbidities using different statistical approaches taking into account age and gender. It allows the user to provide its own clinical record data that should follow a simple tabulated format. In addition, the package allows the analysis of the temporal directionality of the co-occurring diseases. A special focus is made on the visualization of the results, providing a variety of representation formats, such as networks, heatmaps or bar plots. The package is available at bitbucket.